Raw data visualization
median
0.0
0.1
0.2
0.3
0.4
6
8
10
log(intensity)
density
sample
10amol_1
10amol_2
10amol_3
10amol_4
50amol_1
50amol_3
50amol_2
50amol_4
100amol_1
100amol_3
100amol_2
100amol_4
250amol_1
250amol_2
250amol_3
250amol_4
500amol_1
500amol_3
500amol_2
500amol_4
1fmol_1
1fmol_2
1fmol_3
1fmol_4
5fmol_1
5fmol_3
5fmol_2
5fmol_4
10fmol_1
10fmol_2
10fmol_3
10fmol_4
25fmol_1
25fmol_2
25fmol_3
25fmol_4
50fmol_1
50fmol_2
50fmol_3
50fmol_4
Intensity distribution over all samples
Save figure
6
8
10
10amol_1
10amol_2
10amol_3
10amol_4
50amol_1
50amol_3
50amol_2
50amol_4
100amol_1
100amol_3
100amol_2
100amol_4
250amol_1
250amol_2
250amol_3
250amol_4
500amol_1
500amol_3
500amol_2
500amol_4
1fmol_1
1fmol_2
1fmol_3
1fmol_4
5fmol_1
5fmol_3
5fmol_2
5fmol_4
10fmol_1
10fmol_2
10fmol_3
10fmol_4
25fmol_1
25fmol_2
25fmol_3
25fmol_4
50fmol_1
50fmol_2
50fmol_3
50fmol_4
log(intensity)
Intensity distribution in each sample
Save figure
10amol_1
10amol_2
10amol_3
10amol_4
50amol_1
50amol_3
50amol_2
50amol_4
100amol_1
100amol_3
100amol_2
100amol_4
250amol_1
250amol_2
250amol_3
250amol_4
500amol_1
500amol_3
500amol_2
500amol_4
1fmol_1
1fmol_2
1fmol_3
1fmol_4
5fmol_1
5fmol_3
5fmol_2
5fmol_4
10fmol_1
10fmol_2
10fmol_3
10fmol_4
25fmol_1
25fmol_2
25fmol_3
25fmol_4
50fmol_1
50fmol_2
50fmol_3
50fmol_4
10amol_1
10amol_2
10amol_3
10amol_4
50amol_1
50amol_3
50amol_2
50amol_4
100amol_1
100amol_3
100amol_2
100amol_4
250amol_1
250amol_2
250amol_3
250amol_4
500amol_1
500amol_3
500amol_2
500amol_4
1fmol_1
1fmol_2
1fmol_3
1fmol_4
5fmol_1
5fmol_3
5fmol_2
5fmol_4
10fmol_1
10fmol_2
10fmol_3
10fmol_4
25fmol_1
25fmol_2
25fmol_3
25fmol_4
50fmol_1
50fmol_2
50fmol_3
50fmol_4
0.95
0.96
0.97
0.98
0.99
1.00
Coefficient
Sample correlation
Save figure
0
1000
2000
3000
10amol_1
10amol_2
10amol_3
10amol_4
50amol_1
50amol_3
50amol_2
50amol_4
100amol_1
100amol_3
100amol_2
100amol_4
250amol_1
250amol_2
250amol_3
250amol_4
500amol_1
500amol_3
500amol_2
500amol_4
1fmol_1
1fmol_2
1fmol_3
1fmol_4
5fmol_1
5fmol_3
5fmol_2
5fmol_4
10fmol_1
10fmol_2
10fmol_3
10fmol_4
25fmol_1
25fmol_2
25fmol_3
25fmol_4
50fmol_1
50fmol_2
50fmol_3
50fmol_4
count
By matching
By MS/MS
Identification types distribution accross samples
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Normalization
-10 -5 0 5 10amol_1_ratio_5fmol_4 10amol_2_ratio_5fmol_4 10amol_3_ratio_5fmol_4 10amol_4_ratio_5fmol_4 50amol_1_ratio_5fmol_4 50amol_3_ratio_5fmol_4 50amol_2_ratio_5fmol_4 50amol_4_ratio_5fmol_4 100amol_1_ratio_5fmol_4 100amol_3_ratio_5fmol_4 100amol_2_ratio_5fmol_4 100amol_4_ratio_5fmol_4 250amol_1_ratio_5fmol_4 250amol_2_ratio_5fmol_4 250amol_3_ratio_5fmol_4 250amol_4_ratio_5fmol_4 500amol_1_ratio_5fmol_4 500amol_3_ratio_5fmol_4 500amol_2_ratio_5fmol_4 500amol_4_ratio_5fmol_4 1fmol_1_ratio_5fmol_4 1fmol_2_ratio_5fmol_4 1fmol_3_ratio_5fmol_4 1fmol_4_ratio_5fmol_4 5fmol_1_ratio_5fmol_4 5fmol_3_ratio_5fmol_4 5fmol_2_ratio_5fmol_4 10fmol_1_ratio_5fmol_4 10fmol_2_ratio_5fmol_4 10fmol_3_ratio_5fmol_4 10fmol_4_ratio_5fmol_4 25fmol_1_ratio_5fmol_4 25fmol_2_ratio_5fmol_4 25fmol_3_ratio_5fmol_4 25fmol_4_ratio_5fmol_4 50fmol_1_ratio_5fmol_4 50fmol_2_ratio_5fmol_4 50fmol_3_ratio_5fmol_4 50fmol_4_ratio_5fmol_4 log2(ratio) Ratio distribution for each sample
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0.0 0.1 0.2 0.3 0.4 6 8 10 intensity density sample 10amol_1 10amol_2 10amol_3 10amol_4 50amol_1 50amol_3 50amol_2 50amol_4 100amol_1 100amol_3 100amol_2 100amol_4 250amol_1 250amol_2 250amol_3 250amol_4 500amol_1 500amol_3 500amol_2 500amol_4 1fmol_1 1fmol_2 1fmol_3 1fmol_4 5fmol_1 5fmol_3 5fmol_2 5fmol_4 10fmol_1 10fmol_2 10fmol_3 10fmol_4 25fmol_1 25fmol_2 25fmol_3 25fmol_4 50fmol_1 50fmol_2 50fmol_3 50fmol_4 Intensity distribution over all samples after normalization
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6 8 10 10amol_1 10amol_2 10amol_3 10amol_4 50amol_1 50amol_3 50amol_2 50amol_4 100amol_1 100amol_3 100amol_2 100amol_4 250amol_1 250amol_2 250amol_3 250amol_4 500amol_1 500amol_3 500amol_2 500amol_4 1fmol_1 1fmol_2 1fmol_3 1fmol_4 5fmol_1 5fmol_3 5fmol_2 5fmol_4 10fmol_1 10fmol_2 10fmol_3 10fmol_4 25fmol_1 25fmol_2 25fmol_3 25fmol_4 50fmol_1 50fmol_2 50fmol_3 50fmol_4 log10(intensity) Intensity distribution in each sample after normalization
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Normalization method : each intensity is expressed relatively to a reference intensity, as a ratio of intensities. Intensities of the sample with the lowest number of missing values are used as reference intensities. Intensities are then centered by substracting the median of the ratios for each sample.
Missing values imputation
0
50
100
150
200
0
2
4
6
10amol_1
10amol_2
10amol_3
10amol_4
50amol_1
50amol_3
50amol_2
50amol_4
100amol_1
100amol_3
100amol_2
100amol_4
250amol_1
250amol_2
250amol_3
250amol_4
500amol_1
500amol_3
500amol_2
500amol_4
1fmol_1
1fmol_2
1fmol_3
1fmol_4
5fmol_1
5fmol_3
5fmol_2
5fmol_4
10fmol_1
10fmol_2
10fmol_3
10fmol_4
25fmol_1
25fmol_2
25fmol_3
25fmol_4
50fmol_1
50fmol_2
50fmol_3
50fmol_4
Count
Frenquency (%)
Missing values distribution accross samples
Save figure
0
500
1000
1500
2000
0
20
40
60
80
0
10
20
30
40
Number of NA values
Number of proteins
Frenquency (%)
Missing values distribution accross proteins
Save figure
0
40000
80000
120000
6
8
10
log(intensity)
count
imputed
FALSE
TRUE
Log intensities distribution with imputed values
Save figure Missing values are imputed with the gaussian model implemented in the library.
Dimension reduction
96%
1.9%
0.2%
0.1%
0.1%
0.1%
0.1%
0.1%
0.1%
0.1%
0
25
50
75
100
1
2
3
4
5
6
7
8
9
10
Dimensions
Percentage of explained variances
Inertia
Save figure
0
5
-20
-10
0
10
Axis1
Axis2
0
10
20
30
Missing_values
Projection of proteins
Save figure
10amol_1_norm
10amol_2_norm
10amol_3_norm
10amol_4_norm
50amol_1_norm
50amol_3_norm
50amol_2_norm
50amol_4_norm
100amol_1_norm
100amol_3_norm
100amol_2_norm
100amol_4_norm
250amol_1_norm
250amol_2_norm
250amol_3_norm
250amol_4_norm
500amol_1_norm
500amol_3_norm
500amol_2_norm
500amol_4_norm
1fmol_1_norm
1fmol_2_norm
1fmol_3_norm
1fmol_4_norm
5fmol_1_norm
5fmol_3_norm
5fmol_2_norm
5fmol_4_norm
10fmol_1_norm
10fmol_2_norm
10fmol_3_norm
10fmol_4_norm
25fmol_1_norm
25fmol_2_norm
25fmol_3_norm
25fmol_4_norm
50fmol_1_norm
50fmol_2_norm
50fmol_3_norm
50fmol_4_norm
-1.0
-0.5
0.0
0.5
1.0
-1.0
-0.5
0.0
0.5
1.0
Dim1 (96%)
Dim2 (1.9%)
2.488
2.492
2.496
2.500
2.504
contrib
Samples contribution
Save figure
10amol_1
10amol_2
10amol_3
10amol_4
50amol_1
50amol_3
50amol_2
50amol_4
100amol_1
100amol_3
100amol_2
100amol_4
250amol_1
250amol_2
250amol_3
250amol_4
500amol_1
500amol_3
500amol_2
500amol_4
1fmol_1
1fmol_2
1fmol_3
1fmol_4
5fmol_1
5fmol_3
5fmol_2
5fmol_4
10fmol_1
10fmol_2
10fmol_3
10fmol_4
25fmol_1
25fmol_2
25fmol_3
25fmol_4
50fmol_1
50fmol_2
50fmol_3
50fmol_4
-0.1
0.0
0.1
0.2
-1.00
-0.75
-0.50
-0.25
0.00
PC1 [96%]
PC2 [2%]
Samples projection
Save figure
Hierarchical clustering
500amol_2
1fmol_2
500amol_1
1fmol_1
500amol_3
1fmol_3
500amol_4
1fmol_4
10amol_3
250amol_4
50amol_4
10amol_4
100amol_4
10amol_1
50amol_1
100amol_1
250amol_1
250amol_3
50amol_3
100amol_3
50amol_2
250amol_2
10amol_2
100amol_2
50fmol_4
50fmol_1
50fmol_2
50fmol_3
25fmol_2
25fmol_3
5fmol_4
5fmol_3
10fmol_3
5fmol_1
5fmol_2
10fmol_4
25fmol_4
25fmol_1
10fmol_1
10fmol_2
Sample
Protein
5
6
7
8
9
log_intensity
Save figure